In an elevator Nina Sharp, the owner of Massive Dynamics, is shot by David Jones but survives. She had been awaited by a group of men wearing masks, one, Jones, wore bandages. Jones did something to her artificial arm while she was unconscious. He is working for Bell Olivia Dunham suspects. The team is worried about Walter Bishop, Peter’s father, too, he did not show up all day.

Olivia suspects William Bell to be behind all that. He had worked together with Walter Bishop on the same project.
"William Bell is not the problem, he is certainly not the head of any terrorist organization", Nina says. "It is true Jones worked for Bell 15 years ago. In fact he was one of our employees in Massive Dynamic." Dunham learns that Jones was unhappy because they had made him go.

William was a father figure to him, a respected mentor. All the destruction Jones did was to prove to William Bell that he was special. Jones had broken out of prison and permanently phoned Massive Dynamics urging them to put him in contact with Bell.

When agent Dunham suggests that Bell needs protection, she learns that he cannot be reached by Jones. "Where is he?", she asks. Nina shakes her head. Bell only communicated with her for months. And Nina is sure: Speaking with William Bell has become more than a professional matter for Dunham. She orders her: "Stop Jones and I will personally arrange a meeting with you and William Bell. But if Jones gets to Bell first, I am afraid all the answers you are searching for die with him."  

 Dunham asks what Jones wanted from Nina. "He stole a very powerful energy cell which Bell hid within my arm."
"What can he do with it?" Dunham asks.  
"Unfortunately the question is: ‘What can’t he do?’ ", Nina responds.

In this moment Jones inserts the cell into machine. He and his men have put up a screen at a crossing in town. They aim for a lorry coming in, but the machine does not work to their content. They achieve to make the machine operating after the lorry nearly has passed the point they aimed at. At this point the air looks blurred. Suddenly the end of the lorry is missing. What is now the rear part of the lorry is sanding on the road.

 

At a beach Walter Bishop is shown a coin by the man who brought him there. "There is more than one of everything." He tells him and informs him that this coins the other remembers is from another place and another time. Walter remembers the house they see before them. "I’ve said too much, I’m not supposed to get involved." The first continues. But Walter does not remember what he is searching for. He is left alone and heads for the house.   

At the Harvard University Astrid is asked about Dr. Bishop: "Has he been acting strange lately?"

Charlie and Olivia are at the scene where the lorry accident had happened. People tell them about the machine the men had put up there. The lorry had seemed as going through a window. They confirm the man had worn bandages.

Peter is shown a picture of his father which was taken 3 hours ago near East Douglas in Grafton. Nina offers agents to go, but Peter thinks it is best if he fetches him by himself.

At the truck scene they discover that all the numbers, registration and serial numbers do not exist.
Olivia shows Nina the pictures of the truck. Nina suspects Olivia already knows where William Ball is. Olivia Dunham is totally taken by surprise, ready to turn this world over to find Bell.

"This is the problem, agent Dunham, William Bell is not in this world."
The team discusses "the other version of this planet", trying to understand the situation. "A déjà vu is like a window", Phillip explains. "Like seeing into the other world." Nina knows what Jones is using the energy cell for: trying to get to Bell.

Desperately Walter tries to remember what to search for. All he knows is that it is extremely important. While Peter shares what he remembers from his childhood when they were here, Walter suddenly remembers "I know how he did it." and urgently leaves.

At a soccer field in Providence agent Dunham and Charlie visit a crime scene. A man witnesses a shimmer like big heat and like a window. When they look at the body the head and the shoulder of the dead person are missing, cut off with burning rims. 

Adding up all information about unexplained phenomena agent Dunham finds a connection: A spot where conditions to create a transfer must be in the region the incidents occurred.  
Walter remembers that he and his friend have had glimpses into another world when using LSD. They know that people exist which are slightly different to the people in this world. And he wanted to get there without LSD. Bell has experimented with travelling to an alternate world. He desperately wants to retrieve something from there he had lost.
Peter shares that it is all about finding the right place to cross over.
"Finding the right place is the key." Nina informs the team. Agent Dunham  finds the place Jones is heading for at the map: Reiden Lake.
Also Walter remembers where the spot is where they can go to the other reality. And he has found the plug in a box stored in that house.

Walter and Peter meet agent Olivia and crew at the lake. They see a bright blue light not far away. They arrive in time to prevent Jones to pass into the other world. He is killed in the attempt. Phillip tells Olivia that Massive Dynamics has been told to cease the star investigation of William Bell. "By whom?", agent Denim asks. "That kind of people when they’ll give you an order you don’t question it. I am sorry."

Peter finds a note: His father will be away for some time. The same moment Walter Bishop stands in front of a grave, crying.
The inscription says: Peter Bishop 1978 – 1985.

Agent Dunham gets a call from Nina Sharp: She intends to keep her promise. At the restaurant at the Mitsumi Hotel on Broadway they wanted to meet Nina does not show up. Agent Dunham takes the elevator to leave. For a short moment she has a déjà vu seeing several people which suddenly are gone again. The elevator stops and she enters a bureau. A paper informs about family Obama moving into a newly furbished White House.
 
Slowly a man enters the office: "I have been waiting quite a long time for this." "Where am I? Who are you?" she asks.
Very friendly he answers: "The answer to your fist question is very complicated. The answer to your second: I am William Bell." 

 

Looking out of the window she oversees New York from one of the highest floors of the Twin towers.